I hated, HATED the scene in Superman 3 where the bad guy's secretary gets turned into a robot. That scene gave me nightmares for years. I still shudder thinking about it. In fact, I just shuddered right now typing that.
Hmm, you know that is pretty creepy, but for some reason it doesn't bother me at all. I just see it as some idiotic plot point in a movie that wasn't really that good, and that lady deserved it anyway for wanting to kill Superman by basically asphyxiating him.
The scene in Robocop where the bad guys are basically turning Murphy into ground beef was pretty sickening to me as a kid. Even when I watch it now I realize how graphic that scene is.
Speaking of ground beef, that scene in "Rumble in the Bronx" with Jackie Chan, where that guy gets tossed into the meat grinder and then stuffed into a garbage bag. We don't actually "see" any of it, but the idea of it, yuck!!
And there were 2 McGyver episodes that totally creeped me out. The one with the russian defectors and the spy who was killing them with that remote control (that looked like a flashlight with a big red bulb). I thought it was some type of device that you could kill people with instantaneously without any trace, like a ray gun that would shut you down forever. That scared the shit out of me. (Only later did I find out that the people who were killed had some device surgically rigged to their hearts that would cut the artery or whatever it did, and that wasn't much consolation

). Another McGyver scene that scared the crap outta me was when McGyver is in medieval times with Merlin, and that one bad guy gets tossed into the lava and all you see is the skeleton floating back up to the top. Yeah, that messed me up for a couple of weeks.
The worst offender and most silly one of all was this stupid Disney cartoon where Mickey Mouse turned Donald Duck into a paper cutout and was playing with the cut out and then turned him back to normal. I kept thinking "if he tears that cut out he's essentially
killing Donald Duck!! That makes me sick to this day and I hated Disney for the longest time for that.